Bottom Line:
Homologous genes resulting from allopolyploidy are commonly referred to as 'homoeologs', although this term has not always been used precisely or consistently in the literature.Here we review the definition of homoeology in historical and modern contexts and propose a precise and testable definition highlighting the connection between homoeologs and orthologs.Establishing a precise and evolutionarily meaningful definition of homoeology is essential for understanding the evolutionary consequences of polyploidization.

fig0020: Evolutionary History of an Allopolyploid. An ancestral genome undergoes a speciation event, resulting in two diploid species. The genes, which descended from a common gene in the ancestor, are orthologs. Evolution occurs after speciation, including structural rearrangements, gene duplications, and gene movement. On polyploidization, genes that were once orthologs are now homoeologs. Homoeologous relationships can be one-to-one, one-to-many, or many-to-many depending on the number of duplications since speciation of the progenitors.

Mentions:
Since homoeology is characterized by an initial speciation event, once the progenitor species of the future allopolyploid begin to diverge, the corresponding genes in each new species that descended from a common ancestral gene start diverging in sequence (Figure 2). The sequence divergence will depend on the time since the progenitor divergence and other factors (the same factors that contribute to ortholog divergence such as selection pressure, duplication events, and others). In addition to genic sequence divergence, other scale evolutionary events may occur, including single-gene duplications, deletions, and rearrangements.

fig0020: Evolutionary History of an Allopolyploid. An ancestral genome undergoes a speciation event, resulting in two diploid species. The genes, which descended from a common gene in the ancestor, are orthologs. Evolution occurs after speciation, including structural rearrangements, gene duplications, and gene movement. On polyploidization, genes that were once orthologs are now homoeologs. Homoeologous relationships can be one-to-one, one-to-many, or many-to-many depending on the number of duplications since speciation of the progenitors.

Mentions:
Since homoeology is characterized by an initial speciation event, once the progenitor species of the future allopolyploid begin to diverge, the corresponding genes in each new species that descended from a common ancestral gene start diverging in sequence (Figure 2). The sequence divergence will depend on the time since the progenitor divergence and other factors (the same factors that contribute to ortholog divergence such as selection pressure, duplication events, and others). In addition to genic sequence divergence, other scale evolutionary events may occur, including single-gene duplications, deletions, and rearrangements.

Bottom Line:
Homologous genes resulting from allopolyploidy are commonly referred to as 'homoeologs', although this term has not always been used precisely or consistently in the literature.Here we review the definition of homoeology in historical and modern contexts and propose a precise and testable definition highlighting the connection between homoeologs and orthologs.Establishing a precise and evolutionarily meaningful definition of homoeology is essential for understanding the evolutionary consequences of polyploidization.